beta-alanine biosynthesis IV

gomodel:YeastPathways_PWY-5760-1

Beta-alanine biosynthesis IV in Saccharomyces cerevisiae S288C oxidizes spermine to spermidine, 3-ammoniopropanal, and hydrogen peroxide, then oxidizes 3-ammoniopropanal to beta-alanine through ALD2 or ALD3 aldehyde dehydrogenase activity.

Pathway type

beta alanine biosynthesis

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

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Pathway network

19 nodes · 28 asserted directed edges

Arrows show recorded subject → object relationships, not necessarily metabolic flow. Select a node for details or an arrow for evidence. Scroll, zoom or find a node to explore.

Reaction / activity
Chemical / cofactor
Protein / complex
Cell / process context
Solid arrow: mechanistic relation
Dashed arrow: membership, location or cofactor relation

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Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Saccharomyces cerevisiae S288C `NCBITaxon:559292`	taxon
hydrogen peroxide `CHEBI:16240`	small molecule
beta-alanine zwitterion `CHEBI:57966`	small molecule
beta-alanine biosynthetic process `GO:0019483`	biological process
NAD(1-) `CHEBI:57540`	small molecule
spermine(4+) `CHEBI:45725`	small molecule
3-ammoniopropanal `CHEBI:58374`	small molecule
ALD2 Scer `SGD:S000004780`	protein
water `CHEBI:15377`	small molecule
dioxygen `CHEBI:15379`	small molecule
NADH(2-) `CHEBI:57945`	small molecule
cytosol `GO:0005829`	cellular component
ALD3 Scer `SGD:S000004779`	protein
FMS1 Scer `SGD:S000004622`	protein
spermidine(3+) `CHEBI:57834`	small molecule
cytoplasm `GO:0005737`	cellular component
FAD(3-) `CHEBI:57692`	cofactor
aldehyde dehydrogenase (NAD+) activity `gomodel:3-PROPANAL-DEHYDROGENASE-RXN`	molecular activity
N(1)-acetylpolyamine oxidase activity `gomodel:RXN-9015`	molecular activity
aldehyde dehydrogenase (NAD+) activity `gomodel:YeastPathways_PWY-5760-1/6a46ef0600000716`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
N(1)-acetylpolyamine oxidase activity `gomodel:RXN-9015`	has_output	hydrogen peroxide `CHEBI:16240`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:RXN-9015 RO:0002234 gomodel:CHEBI_16240_RXN-9015. Source location `./YeastPathways_PWY-5760-1.json#/facts/0; endpoint types: /individuals/10/type; /individuals/3/type`
aldehyde dehydrogenase (NAD+) activity `gomodel:3-PROPANAL-DEHYDROGENASE-RXN`	has_output	beta-alanine zwitterion `CHEBI:57966`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:3-PROPANAL-DEHYDROGENASE-RXN RO:0002234 gomodel:CHEBI_57966_3-PROPANAL-DEHYDROGENASE-RXN. Source location `./YeastPathways_PWY-5760-1.json#/facts/1; endpoint types: /individuals/30/type; /individuals/8/type`
N(1)-acetylpolyamine oxidase activity `gomodel:RXN-9015`	part_of	beta-alanine biosynthetic process `GO:0019483`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:RXN-9015 BFO:0000050 gomodel:YeastPathways_PWY-5760-1/YeastPathways_PWY-5760-1. Source location `./YeastPathways_PWY-5760-1.json#/facts/2; endpoint types: /individuals/10/type; /individuals/31/type`
aldehyde dehydrogenase (NAD+) activity `gomodel:3-PROPANAL-DEHYDROGENASE-RXN`	has_input	NAD(1-) `CHEBI:57540`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:3-PROPANAL-DEHYDROGENASE-RXN RO:0002233 gomodel:CHEBI_57540_3-PROPANAL-DEHYDROGENASE-RXN. Source location `./YeastPathways_PWY-5760-1.json#/facts/3; endpoint types: /individuals/30/type; /individuals/5/type`
N(1)-acetylpolyamine oxidase activity `gomodel:RXN-9015`	has_input	spermine(4+) `CHEBI:45725`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:RXN-9015 RO:0002233 gomodel:CHEBI_45725_RXN-9015. Source location `./YeastPathways_PWY-5760-1.json#/facts/4; endpoint types: /individuals/10/type; /individuals/4/type`
aldehyde dehydrogenase (NAD+) activity `gomodel:YeastPathways_PWY-5760-1/6a46ef0600000716`	part_of	beta-alanine biosynthetic process `GO:0019483`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:YeastPathways_PWY-5760-1/6a46ef0600000716 BFO:0000050 gomodel:YeastPathways_PWY-5760-1/6a46ef0600000730. Source location `./YeastPathways_PWY-5760-1.json#/facts/5; endpoint types: /individuals/32/type; /individuals/45/type` gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:YeastPathways_PWY-5760-1/6a46ef0600000716 BFO:0000050 gomodel:YeastPathways_PWY-5760-1/YeastPathways_PWY-5760-1. Source location `./YeastPathways_PWY-5760-1.json#/facts/7; endpoint types: /individuals/32/type; /individuals/31/type`
aldehyde dehydrogenase (NAD+) activity `gomodel:3-PROPANAL-DEHYDROGENASE-RXN`	part_of	beta-alanine biosynthetic process `GO:0019483`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:3-PROPANAL-DEHYDROGENASE-RXN BFO:0000050 gomodel:YeastPathways_PWY-5760-1/YeastPathways_PWY-5760-1. Source location `./YeastPathways_PWY-5760-1.json#/facts/6; endpoint types: /individuals/30/type; /individuals/31/type`
aldehyde dehydrogenase (NAD+) activity `gomodel:YeastPathways_PWY-5760-1/6a46ef0600000716`	has_input	3-ammoniopropanal `CHEBI:58374`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:YeastPathways_PWY-5760-1/6a46ef0600000716 RO:0002233 gomodel:CHEBI_58374_RXN-9015. Source location `./YeastPathways_PWY-5760-1.json#/facts/8; endpoint types: /individuals/32/type; /individuals/9/type`
ALD2 Scer `SGD:S000004780`	enables	aldehyde dehydrogenase (NAD+) activity `gomodel:3-PROPANAL-DEHYDROGENASE-RXN`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:3-PROPANAL-DEHYDROGENASE-RXN RO:0002333 gomodel:YMR170C-MONOMER_3-PROPANAL-DEHYDROGENASE-RXN_controller. Source location `./YeastPathways_PWY-5760-1.json#/facts/9; endpoint types: /individuals/30/type; /individuals/12/type`
N(1)-acetylpolyamine oxidase activity `gomodel:RXN-9015`	has_input	water `CHEBI:15377`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:RXN-9015 RO:0002233 gomodel:CHEBI_15377_RXN-9015. Source location `./YeastPathways_PWY-5760-1.json#/facts/10; endpoint types: /individuals/10/type; /individuals/1/type`
N(1)-acetylpolyamine oxidase activity `gomodel:RXN-9015`	has_input	dioxygen `CHEBI:15379`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:RXN-9015 RO:0002233 gomodel:CHEBI_15379_RXN-9015. Source location `./YeastPathways_PWY-5760-1.json#/facts/11; endpoint types: /individuals/10/type; /individuals/2/type`
N(1)-acetylpolyamine oxidase activity `gomodel:RXN-9015`	has_output	3-ammoniopropanal `CHEBI:58374`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:RXN-9015 RO:0002234 gomodel:CHEBI_58374_RXN-9015. Source location `./YeastPathways_PWY-5760-1.json#/facts/12; endpoint types: /individuals/10/type; /individuals/9/type`
aldehyde dehydrogenase (NAD+) activity `gomodel:3-PROPANAL-DEHYDROGENASE-RXN`	has_output	NADH(2-) `CHEBI:57945`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:3-PROPANAL-DEHYDROGENASE-RXN RO:0002234 gomodel:CHEBI_57945_3-PROPANAL-DEHYDROGENASE-RXN. Source location `./YeastPathways_PWY-5760-1.json#/facts/13; endpoint types: /individuals/30/type; /individuals/7/type`
aldehyde dehydrogenase (NAD+) activity `gomodel:YeastPathways_PWY-5760-1/6a46ef0600000716`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:YeastPathways_PWY-5760-1/6a46ef0600000716 BFO:0000066 gomodel:YeastPathways_PWY-5760-1/6a46ef0600000723. Source location `./YeastPathways_PWY-5760-1.json#/facts/14; endpoint types: /individuals/32/type; /individuals/38/type`
aldehyde dehydrogenase (NAD+) activity `gomodel:3-PROPANAL-DEHYDROGENASE-RXN`	has_input	3-ammoniopropanal `CHEBI:58374`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:3-PROPANAL-DEHYDROGENASE-RXN RO:0002233 gomodel:CHEBI_58374_RXN-9015. Source location `./YeastPathways_PWY-5760-1.json#/facts/15; endpoint types: /individuals/30/type; /individuals/9/type`
aldehyde dehydrogenase (NAD+) activity `gomodel:3-PROPANAL-DEHYDROGENASE-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:3-PROPANAL-DEHYDROGENASE-RXN BFO:0000066 gomodel:reaction_3-PROPANAL-DEHYDROGENASE-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY-5760-1.json#/facts/16; endpoint types: /individuals/30/type; /individuals/28/type`
aldehyde dehydrogenase (NAD+) activity `gomodel:YeastPathways_PWY-5760-1/6a46ef0600000716`	has_input	NAD(1-) `CHEBI:57540`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:YeastPathways_PWY-5760-1/6a46ef0600000716 RO:0002233 gomodel:YeastPathways_PWY-5760-1/6a46ef0600000717. Source location `./YeastPathways_PWY-5760-1.json#/facts/17; endpoint types: /individuals/32/type; /individuals/33/type`
aldehyde dehydrogenase (NAD+) activity `gomodel:YeastPathways_PWY-5760-1/6a46ef0600000716`	has_input	water `CHEBI:15377`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:YeastPathways_PWY-5760-1/6a46ef0600000716 RO:0002233 gomodel:YeastPathways_PWY-5760-1/6a46ef0600000718. Source location `./YeastPathways_PWY-5760-1.json#/facts/18; endpoint types: /individuals/32/type; /individuals/34/type`
aldehyde dehydrogenase (NAD+) activity `gomodel:3-PROPANAL-DEHYDROGENASE-RXN`	has_input	water `CHEBI:15377`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:3-PROPANAL-DEHYDROGENASE-RXN RO:0002233 gomodel:CHEBI_15377_3-PROPANAL-DEHYDROGENASE-RXN. Source location `./YeastPathways_PWY-5760-1.json#/facts/19; endpoint types: /individuals/30/type; /individuals/0/type`
ALD3 Scer `SGD:S000004779`	enables	aldehyde dehydrogenase (NAD+) activity `gomodel:YeastPathways_PWY-5760-1/6a46ef0600000716`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:YeastPathways_PWY-5760-1/6a46ef0600000716 RO:0002333 gomodel:YeastPathways_PWY-5760-1/6a46ef0600000722. Source location `./YeastPathways_PWY-5760-1.json#/facts/20; endpoint types: /individuals/32/type; /individuals/37/type`
N(1)-acetylpolyamine oxidase activity `gomodel:RXN-9015`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:RXN-9015 BFO:0000066 gomodel:reaction_RXN-9015_location_lociGO_0005829. Source location `./YeastPathways_PWY-5760-1.json#/facts/21; endpoint types: /individuals/10/type; /individuals/29/type`
aldehyde dehydrogenase (NAD+) activity `gomodel:YeastPathways_PWY-5760-1/6a46ef0600000716`	has_output	NADH(2-) `CHEBI:57945`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:YeastPathways_PWY-5760-1/6a46ef0600000716 RO:0002234 gomodel:YeastPathways_PWY-5760-1/6a46ef0600000720. Source location `./YeastPathways_PWY-5760-1.json#/facts/22; endpoint types: /individuals/32/type; /individuals/36/type`
FMS1 Scer `SGD:S000004622`	enables	N(1)-acetylpolyamine oxidase activity `gomodel:RXN-9015`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:RXN-9015 RO:0002333 gomodel:YMR020W-MONOMER_RXN-9015_controller. Source location `./YeastPathways_PWY-5760-1.json#/facts/23; endpoint types: /individuals/10/type; /individuals/11/type`
aldehyde dehydrogenase (NAD+) activity `gomodel:YeastPathways_PWY-5760-1/6a46ef0600000716`	has_output	beta-alanine zwitterion `CHEBI:57966`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:YeastPathways_PWY-5760-1/6a46ef0600000716 RO:0002234 gomodel:YeastPathways_PWY-5760-1/6a46ef0600000719. Source location `./YeastPathways_PWY-5760-1.json#/facts/24; endpoint types: /individuals/32/type; /individuals/35/type`
N(1)-acetylpolyamine oxidase activity `gomodel:RXN-9015`	has_output	spermidine(3+) `CHEBI:57834`	gomodel:YeastPathways_PWY-5760-1 Source assertion: The model asserts gomodel:RXN-9015 RO:0002234 gomodel:CHEBI_57834_RXN-9015. Source location `./YeastPathways_PWY-5760-1.json#/facts/25; endpoint types: /individuals/10/type; /individuals/6/type`
ALD2 Scer `SGD:S000004780`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:11914276)	cytoplasm `GO:0005737`	UniProtKB:P47771 Source assertion: UniProtKB:P47771 annotates location Cytoplasm (SL-0086). Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_subcellular_location%2Ccc_function%2Ccc_caution%2Corganism_id#/results/3891/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P47771 Source assertion: UniProtKB:P47771 has the exact SGD cross-reference SGD:S000004780. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_subcellular_location%2Ccc_function%2Ccc_caution%2Corganism_id#/results/3891/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
ALD3 Scer `SGD:S000004779`	located_in Physical protein location from reviewed UniProt. ECO:0000250	cytoplasm `GO:0005737`	UniProtKB:P54114 Source assertion: UniProtKB:P54114 annotates location Cytoplasm (SL-0086). Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_subcellular_location%2Ccc_function%2Ccc_caution%2Corganism_id#/results/4024/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P54114 Source assertion: UniProtKB:P54114 has the exact SGD cross-reference SGD:S000004779. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_subcellular_location%2Ccc_function%2Ccc_caution%2Corganism_id#/results/4024/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
FMS1 Scer `SGD:S000004622`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000269 (PubMed:12670477) Binds 1 FAD per subunit. UniProt note evidence: ECO:0000269 (PubMed:12670477)	FAD(3-) `CHEBI:57692`	UniProtKB:P50264 Source assertion: UniProtKB:P50264 annotates CHEBI:57692 as a cofactor of this protein. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_cofactor%2Corganism_id%2Ccc_caution [sha256:1378282d22c5518215707964664b55946f468ba74a227a6ea1bbf27db69ddbc4] #/results/3912/comments/0/cofactors/0; /results/3912/comments/0/note` UniProtKB:P50264 Source assertion: UniProtKB:P50264 has the exact SGD cross-reference SGD:S000004622. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_cofactor%2Corganism_id%2Ccc_caution [sha256:1378282d22c5518215707964664b55946f468ba74a227a6ea1bbf27db69ddbc4] #/results/3912/uniProtKBCrossReferences/0`

References

gomodel:YeastPathways_PWY-5760-1 GO-CAM beta-alanine biosynthesis IV model YeastPathways_PWY-5760-1 (source version: Pinned Noctua JSON archive; model date 2026-07-06; member ./YeastPathways_PWY-5760-1.json)
UniProtKB:P47771 Reviewed UniProtKB P47771 location annotations (source version: UniProt release 2026_03)
UniProtKB:P54114 Reviewed UniProtKB P54114 location annotations (source version: UniProt release 2026_03)
UniProtKB:P50264 UniProtKB P50264 cofactor annotations (source version: 2026_03)

Curation history

2026-10-05T06:05:08Z Codex; review-causal-graph; Reviewed every native GO-CAM fact; preserved precise input/output, causal, location, membership and complex-part relations with traceable structured source evidence. Kept distinct generic physical instances and recorded source-scope exclusions in the cohort review ledger.
2026-10-05T06:43:56Z Codex
- EDIT — Audit causal activity compartments and preserve scoped protein location evidence
  Reviewed all 3 activity location assignments and 3 mapped physical proteins against reviewed S288C UniProt release2026_03 location/function/caution batch SHA256 95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d. Added 2 independently supported location edges and quarantined 0 generic cytosol source assertions. Mapped physical protein locations via exact SGD cross-references; retained source ECO grades, molecular form and conditional notes. Physical protein location alone never generates activity location. Explicitly inspected functional assertions support bounded activity projections. Every original activity location and exclusion is recorded in reports/causal_graph_review/gocam-location-review.json. No independent location annotation is treated as an evidence gap, not a negative result. Cytoplasm is not narrowed to cytosol. Microsome fractions are not projected as in-vivo organelles. Semantic validation passed all85 records;4 independent source-role acceptance tests passed.
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